Sofía Cano , María Ángeles Clari , Javier Colomina , Laura García , Cristina Sanchís- Piqueras , Ignacio Torres , Gerardo Aguilar , Nieves Carbonell , David Navarro
{"title":"Off-label use of the BIOFIRE® Blood Culture Identification 2 Panel for multidrug-resistant bacteria colonization surveillance in critical care unit patients: A retrospective study","authors":"Sofía Cano , María Ángeles Clari , Javier Colomina , Laura García , Cristina Sanchís- Piqueras , Ignacio Torres , Gerardo Aguilar , Nieves Carbonell , David Navarro","doi":"10.1016/j.diagmicrobio.2025.116930","DOIUrl":"10.1016/j.diagmicrobio.2025.116930","url":null,"abstract":"<div><div>In this retrospective, single-center, observational study we assessed the performance of the BIOFIRE® Blood Culture Identification 2 (BCID2) Panel for the identification of multidrug-resistant bacteria (MDRB)-colonized critical care unit patients compared with a standard culture and antimicrobial susceptibility testing (AST)-based approach. A total of 146 rectal/pharyngeal/nasal combined specimens from 130 patients were tested by using the BCID2 panel. MDRB were detected in 40/146 (27.3%) specimens from 39 patients (30%) by the BCID2 panel; MDRB were recovered by culture in 32/146 (21.9%) specimens from 30 patients (23%). Concordance between the MDRB detected by the BCID2 panel and those recovered by culture was observed in 29/43 cases; MDRB were more frequently extended-spectrum beta-lactamase-harboring Enterobacterales or <em>van</em>A/B-carrying <em>Enterococcus faecium</em>. The per specimen positive and negative percentage agreement values were 90.6% and 90.3%, respectively (Kappa value: 0.73). The BCID2 panel shows promise as a tool for the rapid identification of MDRB carriers in critical care units. Its use may lead to prescription of more refined empirical antimicrobial therapies on an individual basis and allow timely isolation of patients to prevent MDRB spreading. Nevertheless, larger, multicenter, prospective, and Next-generation sequencing-validated studies are needed to corroborate our findings.</div></div>","PeriodicalId":11329,"journal":{"name":"Diagnostic microbiology and infectious disease","volume":"113 2","pages":"Article 116930"},"PeriodicalIF":2.1,"publicationDate":"2025-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144169110","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"CMV retinitis in HIV-infected patients: Plasma viral load utility in diagnosis","authors":"Samia Benadda , Nassima Achour , Hanifa Ziane , Kamal Kezzal","doi":"10.1016/j.diagmicrobio.2025.116926","DOIUrl":"10.1016/j.diagmicrobio.2025.116926","url":null,"abstract":"<div><h3>Objectives</h3><div>This study evaluates the role of CMV plasma viral load in diagnosing retinitis among Algerian HIV patients.</div></div><div><h3>Methods</h3><div>Simultaneous ophtalmologic examination and CMV plasma viral load testing were conducted for 40 HIV patients with vision issues. Plasma viral load kinetics was determined during treatment, and in case of persistent viral load, resistance genotyping was performed.</div></div><div><h3>Results</h3><div>Viral load findings correlated with ophtalmic examination results in 75 % of cases. Four (04) retinitis cases had undetectable viral loads. Virological monitoring identified Algeria's first ganciclovir-resistant CMV strain.</div></div><div><h3>Conclusion</h3><div>Plasma viral load testing is a valuable diagnostic tool but cannot replace ophthalmic examination. Quantitative PCR aids in effective virological monitoring and timely treatment initiation.</div></div>","PeriodicalId":11329,"journal":{"name":"Diagnostic microbiology and infectious disease","volume":"113 2","pages":"Article 116926"},"PeriodicalIF":2.1,"publicationDate":"2025-05-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144169109","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Ziyu Liu , Keqiang Yan , Jing Li , Ce Zhang , Donghao Xu , Yuhan Wang , Xiaomei Xie , Haiyan Li , Jiarong Qie , Jinxin Li , Xiaofei Dong , Liang Dong , Hualei Cui
{"title":"Acute appendicitis in children: Two microbial states associated with clinical indicators and severity","authors":"Ziyu Liu , Keqiang Yan , Jing Li , Ce Zhang , Donghao Xu , Yuhan Wang , Xiaomei Xie , Haiyan Li , Jiarong Qie , Jinxin Li , Xiaofei Dong , Liang Dong , Hualei Cui","doi":"10.1016/j.diagmicrobio.2025.116925","DOIUrl":"10.1016/j.diagmicrobio.2025.116925","url":null,"abstract":"<div><h3>Background</h3><div>Acute appendicitis (AA) is one of the most common abdominal emergencies worldwide. It is associated with dysbiosis and is usually classified clinically as either simple appendicitis (SA) or complicated appendicitis (CA) . The etiology and pathogenesis of AA remain incompletely understood.</div></div><div><h3>Methods</h3><div>A total of 74 pediatric intra-abdominal pus samples from appendectomy cases (aged 3-15) were collected for AA at Tianjin Children's Hospital (Feb 2022-Sep 2023). The samples were categorised into two groups based on pathological findings: SA (n = 27) and CA (n = 47). Metagenomic profiling was employed to characterized the microbial composition and function in both groups. Additionally, clinical parameters associated with the microbiota were analysed.</div></div><div><h3>Results</h3><div>The SA group exhibited higher levels of <em>Burkholderia, Mycobacterium</em>, and <em>Klebsiella</em>, while the CA group demonstrated higher levels of <em>Porphyromonas, Bacteroides, Fusobacterium, Prevotella</em>, and <em>Tannerella</em>. Additionaly, there were significant differences in clinical parameters, including C-reactive protein (CRP), procalcitonin (PCT), fibrinogen, sodium, potassium, phosphorus, complement C3, and chloride, between two groups. Furthermore, functional profiling revealed alterations in microbial metabolism and antibiotic resistance, highlighting the complex interplay between microbial communities and host inflammatory responses in appendicitis.</div></div><div><h3>Conclusions</h3><div>This study identifies unique microbial and serum biomarkers and their correlates in varying severities of acute appendicitis, highlighting the role of the microbiome in the aetiology of acute appendicitis.</div></div>","PeriodicalId":11329,"journal":{"name":"Diagnostic microbiology and infectious disease","volume":"113 2","pages":"Article 116925"},"PeriodicalIF":2.1,"publicationDate":"2025-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144138448","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Mingyang wang , Ying Ma , Nina Zhang, Li Li, Yurong Fu, li’an Li, Qingzhi Zhai
{"title":"Methylation testing versus cervical cytology for triage of HPV-positive women: A comparative study","authors":"Mingyang wang , Ying Ma , Nina Zhang, Li Li, Yurong Fu, li’an Li, Qingzhi Zhai","doi":"10.1016/j.diagmicrobio.2025.116917","DOIUrl":"10.1016/j.diagmicrobio.2025.116917","url":null,"abstract":"<div><h3>Background</h3><div>In many countries, HPV testing has replaced cervical cytology as the primary screening method for cervical cancer. While HPV testing has high sensitivity, its limited specificity necessitates triage to reduce unnecessary colposcopy referrals. This study evaluates the performance of cervical cytology (TCT) and the GynTect® six-gene methylation test as triage methods for HPV-positive women.</div></div><div><h3>Methods</h3><div>A total of 276 women from China were categorized into four pathological groups: cervical squamous cell carcinoma (CSCC), CIN3, CIN2, and CIN1. The diagnostic performance of TCT and the GynTect test was assessed for detecting CIN3+, with sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) calculated for both methods.</div></div><div><h3>Results</h3><div>Abnormal cytology (ASC-US+) had a sensitivity of 71.9% and specificity of 75.0% for detecting CIN3+, with a PPV of 57.5% and NPV of 85.0%. In comparison, the GynTect test demonstrated superior diagnostic accuracy, with a sensitivity of 88.5%, specificity of 87.2%, PPV of 78.7%, and NPV of 93.5%. The GynTect test outperformed cytology in identifying CIN3+ while reducing unnecessary colposcopies in women with CIN2- lesions.</div></div><div><h3>Conclusions</h3><div>The GynTect six-gene methylation test provides higher diagnostic accuracy than cervical cytology in the triage of HPV-positive women. Its superior sensitivity and specificity make it a valuable tool for improving risk stratification in HPV-based cervical cancer screening. These findings support the integration of methylation-based testing into screening programs to enhance diagnostic precision and optimize patient management.</div></div>","PeriodicalId":11329,"journal":{"name":"Diagnostic microbiology and infectious disease","volume":"113 2","pages":"Article 116917"},"PeriodicalIF":2.1,"publicationDate":"2025-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144169282","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Sadia Almas , Rob E. Carpenter , Vaibhav K. Tamrakar , Aditya Sharma , Kamalpreet Suri , Salima Karki , Katelyn Kyser , Randy Sronce , Rahul Sharma
{"title":"Streamlining fungal diagnostics: Evaluation of a Direct-to-PCR extraction-free workflow for candida detection","authors":"Sadia Almas , Rob E. Carpenter , Vaibhav K. Tamrakar , Aditya Sharma , Kamalpreet Suri , Salima Karki , Katelyn Kyser , Randy Sronce , Rahul Sharma","doi":"10.1016/j.diagmicrobio.2025.116923","DOIUrl":"10.1016/j.diagmicrobio.2025.116923","url":null,"abstract":"<div><div>Fungal infections are an escalating health threat, and delays from conventional nucleic acid extraction hinder timely diagnosis and treatment. This study evaluated the diagnostic performance of a novel extraction-free technology, Direct-to-PCR (D2P; Scienetix, Tyler, TX, USA), for the detection of clinically significant <em>Candida</em> species (<em>C. albicans, C. glabrata, C. auris, C. parapsilosis</em>, and <em>C. tropicalis</em>). D2P was compared against conventional silica column-based (Qiagen) and magnetic bead-based (KingFisher) extraction methods, using microbial reference isolates, residual clinical specimens, and limit-of-detection analyses. Diagnostic sensitivity and specificity of D2P were comparable to conventional approaches, with specificity ranging from 96.77 % to 100 %. Concordance between methods was high, with Cohen’s kappa coefficients (κ=0.93–1.00). Limit-of-detection analyses demonstrated strong analytical sensitivity, with excellent linearity (R²=0.924–0.999) and low replicate variability (coefficient of variation 0.2–6.3 %). Statistical comparison of cycle threshold values revealed no significant differences between methods (<em>p</em> > 0.05), supporting equivalent nucleic acid recovery without the need for time-intensive extraction steps. Despite these strengths, the study has limitations. The relatively small number of residual clinical specimens (<em>n</em> = 40) may restrict the generalizability of findings, and further validation across broader patient populations, specimen types, and clinical settings is warranted. Nevertheless, D2P offers a streamlined, rapid diagnostic workflow that reduces turnaround times and enhances accessibility, particularly in resource-limited environments. Wider adoption of extraction-free PCR platforms such as D2P could facilitate earlier detection of invasive candidiasis, improve clinical outcomes, and mitigate healthcare-associated morbidity and mortality attributable to fungal infections.</div></div>","PeriodicalId":11329,"journal":{"name":"Diagnostic microbiology and infectious disease","volume":"113 2","pages":"Article 116923"},"PeriodicalIF":2.1,"publicationDate":"2025-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144138274","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Diagnostic performance of an in-house real-time polymerase chain reaction (PCR) assay and antigen detection from respiratory samples for the diagnosis of pulmonary cryptococcosis","authors":"Karthick Kumar , Hansraj Choudhary , Haseen Ahmad , Valliappan Muthu , Parikshaa Gupta , Shivaprakash M Rudramurthy , Sourav Agnihotri , Ritesh Agarwal , Arunaloke Chakrabarti , Harsimran Kaur","doi":"10.1016/j.diagmicrobio.2025.116924","DOIUrl":"10.1016/j.diagmicrobio.2025.116924","url":null,"abstract":"<div><h3>Introduction</h3><div>The currently available diagnostic tests lack sensitivity to diagnose pulmonary cryptococcosis. In the current study, we developed and standardized an in-house real-time PCR assay and evaluated the antigen detection in respiratory samples for the diagnosis of pulmonary cryptococcosis.</div></div><div><h3>Materials and Methods</h3><div>We standardized an in-house real-time PCR assay (using URA5 and STR1 primers; index test 1) and cryptococcal antigen detection (BIOSYNEX® CryptoPS, France) from the respiratory samples (index test 2). We considered a sample positive for PCR assay when both gene targets (URA5 and STR1) were detected. We prospectively enrolled subjects undergoing evaluation for non-resolving pneumonia and evaluated the performance of the index tests for diagnosing pulmonary cryptococcosis. The reference standard was proven or probable pulmonary cryptococcosis diagnosed by EORTC/MSG (European Organization for Research and Treatment of Cancer/ Mycoses Study Group) criteria.</div></div><div><h3>Results</h3><div>Of the 133 subjects enrolled in the study, two (2.66 %) and three (3.99 %) were diagnosed as having proven and probable pulmonary cryptococcosis. 3.8 % of study subjects had HIV. The sensitivity and specificity of qPCR (index test 1) for the diagnosis of pulmonary cryptococcosis were 60.0 % (95 % CI: 14.6-94.7) and 96.1 % (95 % CI: 91.1-98.7), respectively, while the sensitivity and specificity of antigen detection from respiratory samples (index test 2) were 40.0 % (95 % CI: 5.2-85.3) and 99.2 % (95 % CI: 95.7 -100.0), respectively.</div></div><div><h3>Discussion</h3><div>In-house PCR and antigen detection in respiratory specimens can potentially be used for early diagnosis of pulmonary cryptococcosis. Larger multicenter studies are required to confirm their utility.</div></div>","PeriodicalId":11329,"journal":{"name":"Diagnostic microbiology and infectious disease","volume":"113 2","pages":"Article 116924"},"PeriodicalIF":2.1,"publicationDate":"2025-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144169108","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
L. Ruffier d’Epenoux , C. Hervochon , A. Antari , K. Rwayane , A. Paquin , E. Persyn , S. Corvec
{"title":"White blood cell count in biological fluids: development and evaluation using the automated particle-analysis DxUⓇ Iris instrument","authors":"L. Ruffier d’Epenoux , C. Hervochon , A. Antari , K. Rwayane , A. Paquin , E. Persyn , S. Corvec","doi":"10.1016/j.diagmicrobio.2025.116906","DOIUrl":"10.1016/j.diagmicrobio.2025.116906","url":null,"abstract":"<div><h3>Background</h3><div>Cytological analysis of serous fluids is critical for the diagnosis and therapeutic management of patients. The \"gold standard\" for cell counting remains manual microscopic counting which is time-consuming and requires skilled and experienced personnel.</div></div><div><h3>Purpose</h3><div>Over an 8-month period, we assessed the performance of automated DxU<sup>Ⓡ</sup> Iris instrument and compared its results with manual microscopic method.</div></div><div><h3>Methods</h3><div>From June 2023 to March 2024, all serous fluids (synovial fluid (SF), peritoneal fluid (PF), pleural fluid (PLF), ascitic fluid (AF), pericardial fluid (PCF), and peritoneal dialysis fluid (PDF)) were included in this study. White blood cell (WBC) counts were performed manually by microscopic method and simultaneously with the DxU<sup>Ⓡ</sup> Iris. For automated analysis, the sample dilution was adjusted according to the appearance of the specimen. Hyaluronidase crystals were added to viscous SF.</div></div><div><h3>Results</h3><div>A total of 739 body fluids were included: 150 SF, 200 PF, 200 PLF, 150 AF, 33 PCF, and 6 PDF. The agreement between the automated method and the manual reference showed a high correlation, with R² values of 0.943 for SF, 0.908 for PF, 0.756 for PLF, 0.992 for AF, 0.968 for PCF and 0.954 for PDF. In addition, results for body fluid samples from oncologic patients showed no difference between both methods.</div></div><div><h3>Conclusion</h3><div>The DxU<sup>Ⓡ</sup> Iris appears to be a promising alternative to the gold standard for cytological analysis of puncture fluids, including in oncology patients. Its implementation, especially for hyaluronidase pre-treated samples, could effectively replace the time-consuming and tedious optical analysis in routine practice.</div></div>","PeriodicalId":11329,"journal":{"name":"Diagnostic microbiology and infectious disease","volume":"113 2","pages":"Article 116906"},"PeriodicalIF":2.1,"publicationDate":"2025-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144138275","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Christine M. Akamine , Kristen A. Staggers , Hana M. El Sahly
{"title":"Prolonged SARS-CoV-2 nucleic acid detection: clinical characteristics from a US hospital","authors":"Christine M. Akamine , Kristen A. Staggers , Hana M. El Sahly","doi":"10.1016/j.diagmicrobio.2025.116921","DOIUrl":"10.1016/j.diagmicrobio.2025.116921","url":null,"abstract":"<div><div>Reports of prolonged SARS-CoV-2 nucleic acid detection have been described. Of 175 adult patients readmitted after being hospitalized with COVID-19 between March 2020 and June 2021, 35 had positive SARS-CoV-2 nucleic acid amplification test (NAAT) 30 days or more from their initial NAAT. Higher albumin levels at the initial hospitalization were associated with a decreased risk of prolonged viral detection.</div></div>","PeriodicalId":11329,"journal":{"name":"Diagnostic microbiology and infectious disease","volume":"113 2","pages":"Article 116921"},"PeriodicalIF":2.1,"publicationDate":"2025-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144169111","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Louise O’Connor , Elizabeth Minogue , Shaunagh Carolan , Gabriel Darcy , Alexandra Chueiri , Muireann Faherty , Joy Morton , Francesca Mc Donagh , Nitin Kumar Singh , Kasthuri Venkateswaran , Georgios Miliotis , Terry J. Smith
{"title":"Rapid detection of the novel human pathogen Pantoea piersonii: advancements in methodology","authors":"Louise O’Connor , Elizabeth Minogue , Shaunagh Carolan , Gabriel Darcy , Alexandra Chueiri , Muireann Faherty , Joy Morton , Francesca Mc Donagh , Nitin Kumar Singh , Kasthuri Venkateswaran , Georgios Miliotis , Terry J. Smith","doi":"10.1016/j.diagmicrobio.2025.116905","DOIUrl":"10.1016/j.diagmicrobio.2025.116905","url":null,"abstract":"<div><div><em>Pantoea piersonii</em> a novel bacterium isolated from the International Space Station (ISS) presents a unique challenge for microbial monitoring in spaceflight and more recently in clinical environments. Identification of the organism currently involves culture, followed by whole genome sequencing and analysis of generated sequences. Since the MALDI-TOF profile of this pathogen is absent from the database and 16S rRNA sequencing fails to resolve its identity to the nearest neighbour, a definitive genetic marker is required for unambiguous identification of the organism. Given the increase in the number of reported clinical cases, there exists a need for a rapid method for identification of the organism which could be utilised in a range of environments including the clinical setting.</div><div>This study describes the design, development and validation of a specific and sensitive real-time PCR assay for the specific detection of <em>P. piersonii.</em> The assay targets a unique region of the malate dehydrogenase gene, confirmed through comparative genomic analysis. We demonstrate the performance of the assay in terms of analytical specificity, sensitivity, and robustness, ensuring its suitability for both space microbiology applications and clinical use.</div></div>","PeriodicalId":11329,"journal":{"name":"Diagnostic microbiology and infectious disease","volume":"113 2","pages":"Article 116905"},"PeriodicalIF":2.1,"publicationDate":"2025-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144169283","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}